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SD CADD meeting: Introduction to the PDB

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Introduction to the PDB

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SD CADD meeting: Introduction to the PDB

  1. 1. RCSB  Protein  Data  Bank   1   Founded in 1998 Rutgers, The State University of New Jersey •  Data deposition & annotation UC San Diego, San Diego Supercomputer Center •  Data dissemination (rcsb.org) Query, analysis, visualization, web services, data download
  2. 2. wwPDB   2   Wellcome Trust, EU, CCP4, BBSRC, MRC, EMBL NLM BIRD-JST, MEXT NSF, NIGMS, DOE, NLM, NCI, NINDS, NIDDK wwPDB formed in 2003 •  Defines data and validation standards •  Collects, annotates, validates and disseminates PDB data
  3. 3. RCSB  PDB  West  Team   §  Science: structural and computational biology, structural bioinformatics, chemoinformatics, genomics, drug design, scientific software development, research grants §  Software: web design, user experience design, database design, web services, big data, open source development §  Systems: hardware, networking, virtualization, cloud computing, data management 3   Scientists, software engineers, postdocs, students
  4. 4. 4  
  5. 5. Growing  User  Base  
  6. 6. Open  Source  Software  Development   § BioJava  (Sequence  and  Structure  modules)   §  https://github.com/biojava   § RCSB  PDB  SpeciNic  Software   §  https://github.com/rcsb     § Macromolecular  Transmission  Format  (MMTF)   §  http://mmtf.rcsb.org   6  

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